The USCBrain atlas is fully compatible with BrainSuite and is included in the default GUI. It can also be used separately with SVReg module in BrainSuite from the command line. Please refer to this.
The USCBrain atlas can be used with FreeSurfer for surface labeling of a given subject. This can be done in the following steps:
- Process the subjct data using freesurfer recon-all pipeline.
- Run the following python code.
freesurfer_label_USCBrain.py <path-to-freesurfer-subject-dir> <path-to-freesurfer-atlas-dir-sphere-map>
Where is shared with this package. The output of the registration is stored as a dfs file that can be visualized in BrainSuite.
FSL can be used with the new atlas to warp atlas labels to the subject labels. This can be done by using FNIRT, the nonlinear registration program that is part of FSL package.
flirt -ref <anat-image BFC file> -in <uscbrain BFC file> -omat <out-mat file>
fnirt --ref=<anat-image BFC file> --in=<uscbrain BFC file> --aff=<out-mat file> --cout=<fnirtcoeff coeff file>
applyxfm --ref=<anat-image BFC file> --in=<uscbrain BFC file> --out=<warped-labels> --coef=<fnirtcoeff coeff file>
Note that execution time for flirt is 5-10 min and fnirt can take upto 1-2 hours.
- FNIRT User guide